Rmarkdown: Word and pdf documents

Microsoft Word

• You can specify it when you create a new rmarkdown document.

• You can also specify it later in the YAML header.

---
title: "rmarkdown_pdf_docx"
author: "Sebastien Renaut"
date: '2018-09-06'
output: word_document
---

• Then, it’s just a matter of kniting the document!

• Little documentation, few options & configurations are possible. (This is not the course of events that should be promoted, as it moves away from an open source environment).

Portable Document Format (.pdf)

• You need a extra step to go from LaTeX (.tex) format to a .pdf. This is handled by the pdflatex function in R.

• LaTeX software is a high-quality typesetting system.

• It is the de facto standard for the communication and publication of scientific documents.

• LaTeX is available as free software.

• Latex software is available here.

• If interested, follow this discussion: Why LaTeX is such a bloated system?

• So…TinyTeX is a custom LaTeX distribution based on TeX Live that is small in size (~150MB) but functions well in most cases, especially for R users .

• tinytex R package is a wrapper function that installs TinyTeX.

Exercice 1 (15min.)

• Install the tinytex R package from the console.

install.packages(“tinytex”)
library(tinytex)
It takes a few minutes to download and compile tinytex (~150MB)
install_tinytex()

• Compile your document as .pdf:

-–
title: “rmarkdown_pdf_docx”
author: “Sebastien Renaut”
date: ‘2018-09-06’
output: pdf_document
-–

More complex header

-–
output
pdf_document:
keep_tex: true
fig_caption: true
latex_engine: pdflatex
title: “This is my first Rmarkdown manuscript”
date: February 05, 2019
geometry: margin=1in
fontfamily: mathpazo
fontsize: 11pt
spacing: double
csl: ../reference_material/peerj.csl
bibliography: ../reference_material/reference.bib
-–

• Note the indentation in the .Rmd document.

• Note the bibliography file and csl file for formatting references.

R packages rticles

• This is a nice package to format articles according to the specification of a journal.

• But first, you need to install it in the R console install.packages("rticles").

```{r rticles, include=T} #install.packages(“rticles”) library(rticles) ```

• Once installed, try starting a new R markdown document according to your journal of interest.

 

 

Template (.tex)

• You can build your own template if you know Latex…

• There are many templates available on the web that you can use.

• Here is one I like for manuscripts (Thanks svmiller!):

• Here is one I like for CVs:

• Simply download it and add it to the YAML header like this: template: ../reference_material/svm-latex-ms.tex
---
output:
pdf_document:
keep_tex: true
fig_caption: true
latex_engine: pdflatex
template: ../reference_material/svm-latex-ms.tex
title: "**This is my first Rmarkdown manuscript**
---

Overleaf

• Overleaf is an online LaTeX and Rich Text collaborative writing and publishing tool that makes the whole process of writing, editing and publishing scientific documents much quicker and easier.

• Remember this:
  

• So you can generate your .tex file, upload it to a github repo and Overleaf will connect to it. Others can then collaborate and modify the .tex file. We will not learn this today, but check:

• A tutorial on how to interface an R Notebook with Overleaf

slide presentation

• You can generate Powerpoint like presentations. We will not learn this today:

Bookdown

https://bookdown.org/

Radix

• https://blog.rstudio.com/2018/09/19/radix-for-r-markdown/

• Stay tuned, as it might replace the ‘rmarkdown’ package…